Activated blood coagulation factor X (FXa) plays a critical initiation step of the blood-coagulation pathway and is considered a desirable target for anticoagulant drug development. It is reversibly inhibited by nonvitamin K antagonist oral anticoagulants (NOACs) such as apixaban, betrixaban, edoxaban, and rivaroxaban. Thrombosis is extremely common and is one of the leading causes of death in developed countries. In previous studies, novel thiourea and oxime ether isosteviol derivatives as FXa inhibitors were designed through a combination of QSAR studies and molecular docking. In the present contribution, molecular dynamics (MD) simulations were performed for 100 ns to assess binding structures previously predicted by docking and furnish additional information. Moreover, three thiourea- and six oxime ether-designed isosteviol analogs were then examined for their drug-like and ADMET properties. MD simulations demonstrated that four out of the nine investigated isosteviol derivatives, i.e., one thiourea and three oxime ether ISV analogs, form stable complexes with FXa. These derivatives interact with FXa in a manner similar to Food and Drug Administration (FDA)-approved drugs like edoxaban and betrixaban, indicating their potential to inhibit factor Xa activity. One of these derivatives, E24, displays favorable pharmacokinetic properties, positioning it as the most promising drug candidate. This, along with the other three derivatives, can undergo further chemical synthesis and bioassessment.

Methylation reactions catalyzed by S-adenosylmethionine (SAM)-dependent methyltransferases are essential to numerous biological functions, including gene expression regulation, epigenetic modifications, and biosynthesis of natural products. Dysregulation of these enzymes is associated with diseases, including cancer and neurodevelopmental disorders, making them attractive drug targets. This review explores the contribution of computational methods, particularly quantum chemical calculations and molecular dynamics (MD) simulations, in elucidating the mechanisms of SAM-dependent methyltransferases. These techniques enable detailed characterization of transition states and reaction pathways, often inaccessible by experimental methods. The review discusses molecular modeling approaches such as the quantum chemical cluster approach (QM-cluster) and hybrid QM/MM methods, emphasizing their applications in studying methyl group transfer, substrate specificity, and the roles of water molecules and metal ions in catalysis. Additionally, dynamic aspects of enzyme function are addressed using classical MD and QM/MM MD simulations. Case studies demonstrate how computational predictions align with experimental data and enable rational design of selective inhibitors and engineered enzymes with altered specificity. Overall, computational chemistry offers a powerful, atomistic view of SAM-dependent methyltransferases, not only complementing experimental studies but also providing a foundation for the design of future experiments in this field.

In this work, the catalytic mechanism of loganic acid methyltransferase was characterized at the molecular level. This enzyme is responsible for the biosynthesis of loganin, which is a precursor for a wide range of biologically active compounds. Due to the lack of detailed knowledge about this process, the aim of this study was the analysis of the structure and activity of loganic acid methyltransferase. Using molecular dynamics (MD) simulations, the native structure of the complex was reconstructed, and the key interactions between the substrate and loganic acid methyltransferase were investigated. Subsequently, the structures obtained from the simulations were used for quantum chemical (QM) calculations. The QM calculations allowed for the exploration of the energetic aspects of the reaction and the characterization of its mechanism. The results obtained in this study suggest the existence of two patterns of interactions between loganic acid methyltransferase and the substrate. The role of residue Q38 in the binding and orientation of the substrate’s carboxyl group was also demonstrated. By employing a combined MD and QM approach, the experimental reaction barrier was reproduced, and detailed insights into the enzymatic activity mechanism of loganic acid methyltransferase were revealed.

Nep1 is a protein essential for the formation of the eukaryotic and archaeal small ribosomal subunit. It is an enzyme responsible for the site–specific SAM–dependent methylation of pseudouridine (Ψ) during the pre–rRNA processing. It possesses a non–trivial topology, namely, a 3 ₁ knot in the active site. Herein, we investigate the structure and mechanism of catalysis of Nep1 using a combination of bioinformatics, computational, and experimental methods. In particular, we address the issue of seemingly unfeasible deprotonation of Ψ nucleobase in the active site of Nep1 by a distant aspartate residue (e.g., D101 in Nep1 of S. cerevisiae ). Sequence alignment analysis across different organisms identifies a conserved serine/threonine residue that may play a role of a proton–transfer mediator (e.g., S233 in Nep1 from S. cerevisiae ), facilitating the reaction. Two enzyme–substrate complexes, one based on an available crystal structure and the other generated by molecular docking, of representative eukaryotic (from S. cerevisiae ) and archaeal (from A. fulgidus ) Nep1 homologs are subjected to molecular dynamics (MD) simulations. The resulting trajectories confirm that the hydroxyl–containing amino acid can indeed adopt a position suitable for proton–shuttling, with the OH group located in between the proton donor and acceptor. However, during the MD simulations, a water molecule emerges from arrangements of the active site, which can assume the role of the proton–transfer mediator instead. To discern between these two alternative pathways, we evaluate the possible methylation mechanisms by quantum–chemical calculations based on density functional theory, using the cluster approach. The obtained energy profiles indicate that the most facile course of the reaction for both the yeast and archaeal enzymes is to engage the water molecule. These results are corroborated by agreement of the computed energy barriers with experimentally measured enzyme kinetics. Moreover, mutational studies show that, while aspartate D101 is crucial for the catalytic activity, serine S233 is irrelevant in this context, indirectly supporting the water–mediated proton transfer. Our findings comprehensively elucidate the mode of action of Nep1 and provide implication for understanding the catalytic mechanisms of other enzymes that involve a proton transfer in the active site over extended distances.